Thanks for the reply. Hmmmm, that does make it hard to see what may be happening. However, try this:

1 : On the page where AEC is loading (with the comments and comment box), view the source code: do you see any multiple (more than one) mentions of "jquery"?

2 : Which other plugins do you have? Some plugin MAY be causing a conflict with AEC (one of the biggest reasons AEC pop-up doesn't show) and related to #1 above.

3 : If you go to Appearance --> Themes, and "Preview" a theme, you can navigate to the comments section OR a single post inside the preview, while logged in as an admin. In any other theme (even TwentyEleven), does the pop-up work?